Analysis of the algorithm: From embeddings to prioritized genes.

The algorithm transformed the similarity matrix to make it compatible with the embedding process. Once this was done for each network and embedding type, it was integrated by embedding type. Below there is a general analysis of the properties of each matrix in the different phases of the process, including the graph building process for each layer.

Annotations Properties

Table 1. Annotation descriptors.

Net Min Max Average Standard_Deviation
DepMap_effect 972 17354 2043.6562906724512 3829.1218209282715
biological_process 1 1053 8.255678448065316 20.730757162592834
cellular_component 1 5172 7.219656420451649 82.56741928666138
disease 1 81 1.7829472267615112 2.3512948371338793
gene_PS 1 108 2.1519058295964126 5.045578888786698
gene_TF 1 5778 3.0320060963993143 74.46796191948712
gene_hgncGroup 1 2294 2.261042369703787 23.27548667222241
hippie_ppi 1 2985 84.68724915097252 150.1286010250888
molecular_function 1 6791 4.87167748867193 54.08093332133869
pathway 1 479 6.75436035343834 16.179001796162975
phenotype 1 1307 23.941396322320227 48.71098651648341
string_ppi 1 7338 610.0699285559645 500.6662722348227

Individual Processing Graph steps

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Embedding Process

Table 2. Uncombined Embedding Matrixes

Net Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero Matrix_Non_Zero_Density
DepMap_effect_pearson ct 17354x17354 301161316 301161316 1.0
DepMap_effect_pearson el 17354x17354 301161316 301161316 1.0
DepMap_effect_pearson ka 17354x17354 301161316 106778670 0.35455639329189276
DepMap_effect_pearson node2vec 17354x17354 301161316 301161316 1.0
DepMap_effect_pearson rf 17354x17354 301161316 301161316 1.0
DepMap_effect_spearman ct 17354x17354 301161316 301161316 1.0
DepMap_effect_spearman el 17354x17354 301161316 301161316 1.0
DepMap_effect_spearman ka 17354x17354 301161316 194719108 0.6465608219084817
DepMap_effect_spearman node2vec 17354x17354 301161316 301161316 1.0
DepMap_effect_spearman rf 17354x17354 301161316 301161316 1.0
biological_process ct 16978x16978 288252484 288252484 1.0
biological_process el 16978x16978 288252484 288252484 1.0
biological_process ka 16978x16978 288252484 257288672 0.8925809360935116
biological_process node2vec 16978x16978 288252484 288252484 1.0
biological_process rf 16978x16978 288252484 288252484 1.0
cellular_component ct 17963x17963 322669369 322669369 1.0
cellular_component el 17963x17963 322669369 322669369 1.0
cellular_component ka 17963x17963 322669369 322669369 1.0
cellular_component node2vec 17963x17963 322669369 322669369 1.0
cellular_component rf 17963x17963 322669369 322669369 1.0
disease ct 4162x4162 17322244 17322244 1.0
disease el 4162x4162 17322244 17322244 1.0
disease ka 4162x4162 17322244 17231758 0.9947763118912307
disease node2vec 4162x4162 17322244 17322244 1.0
disease rf 4162x4162 17322244 17322244 1.0
gene_PS ct 3020x3020 9120400 8927292 0.978826805841849
gene_PS el 3020x3020 9120400 5842664 0.6406148853120477
gene_PS ka 3020x3020 9120400 98718 0.010823867374237971
gene_PS node2vec 3020x3020 9120400 9120400 1.0
gene_PS rf 3020x3020 9120400 5842664 0.6406148853120477
gene_TF ct 3871x3871 14984641 14984637 0.9999997330600046
gene_TF el 3871x3871 14984641 14969165 0.9989672091576969
gene_TF ka 3871x3871 14984641 5275373 0.35205201112258877
gene_TF node2vec 3871x3871 14984641 14984641 1.0
gene_TF rf 3871x3871 14984641 14969165 0.9989672091576969
gene_hgncGroup ct 25136x25136 631818496 631304330 0.9991862124909999
gene_hgncGroup el 25136x25136 631818496 326932198 0.5174463870079549
gene_hgncGroup ka 25136x25136 631818496 14482790 0.022922390040319426
gene_hgncGroup node2vec 25136x25136 631818496 631818492 0.9999999936690679
gene_hgncGroup rf 25136x25136 631818496 326932198 0.5174463870079549
hippie_ppi ct 15763x15763 248472169 248472169 1.0
hippie_ppi el 15763x15763 248472169 245768483 0.9891187571997249
hippie_ppi ka 15763x15763 248472169 421467 0.0016962342370022132
hippie_ppi node2vec 15763x15763 248472169 248472169 1.0
hippie_ppi rf 15763x15763 248472169 245768483 0.9891187571997249
molecular_function ct 17333x17333 300432889 300432889 1.0
molecular_function el 17333x17333 300432889 300432889 1.0
molecular_function ka 17333x17333 300432889 300432889 1.0
molecular_function node2vec 17333x17333 300432889 300432889 1.0
molecular_function rf 17333x17333 300432889 300432889 1.0
pathway ct 5611x5611 31483321 31482925 0.9999874219114305
pathway el 5611x5611 31483321 25851467 0.8211162666098663
pathway ka 5611x5611 31483321 362997 0.011529819233491919
pathway node2vec 5611x5611 31483321 31483321 1.0
pathway rf 5611x5611 31483321 25851467 0.8211162666098663
phenotype ct 5077x5077 25775929 25775929 1.0
phenotype el 5077x5077 25775929 25775929 1.0
phenotype ka 5077x5077 25775929 25756141 0.9992323070101566
phenotype node2vec 5077x5077 25775929 25775929 1.0
phenotype rf 5077x5077 25775929 25775929 1.0
string_ppi ct 18476x18476 341362576 341362576 1.0
string_ppi el 18476x18476 341362576 341362576 1.0
string_ppi ka 18476x18476 341362576 11290078 0.033073566916134355
string_ppi node2vec 18476x18476 341362576 341362576 1.0
string_ppi rf 18476x18476 341362576 341362576 1.0

Table 3. Integrated Embedding Matrixes

Integration Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero Matrix_Non_Zero_Density
integration_mean_by_presence ct 30267x30267 916091289 805232029 0.8789866672337717
integration_mean_by_presence el 30267x30267 916091289 582826435 0.6362099956612511
integration_mean_by_presence ka 30267x30267 916091289 373657315 0.40788218323512515
integration_mean_by_presence node2vec 30267x30267 916091289 805447943 0.879222357718544
integration_mean_by_presence rf 30267x30267 916091289 582826435 0.6362099956612511
mean ct 30267x30267 916091289 805232029 0.8789866672337717
mean el 30267x30267 916091289 582826435 0.6362099956612511
mean ka 30267x30267 916091289 373657315 0.40788218323512515
mean node2vec 30267x30267 916091289 805447943 0.879222357718544
mean rf 30267x30267 916091289 582826435 0.6362099956612511

Weight values